Marek Ostaszewski

28 papers A 5B 1Journal 19Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	KGG: a fully automated workflow for creating disease-specific knowledge graphs. Bioinform. Reagon Karki, Yojana Gadiya, Andrea Zaliani, Bishab Pokharel, Negin Sadat Babaiha, Marek Ostaszewski, Martin Hofmann-Apitius, Philip Gribbon
2024	J	`jnl`	BioKC: a collaborative platform for curation and annotation of molecular interactions. Database J. Biol. Databases Curation Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata P. Satagopam
2024	J	`jnl`	Graph databases in systems biology: a systematic review. Briefings Bioinform. Ilya Mazein, Adrien Rougny, Alexander Mazein, Ron Henkel, Lea Gütebier, Lea Michaelis, Marek Ostaszewski, Reinhard Schneider, Venkata P. Satagopam, Lars Juhl Jensen, Dagmar Waltemath, Judith A. H. Wodke, Irina Balaur
2023	J	`jnl`	A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. Frontiers Bioinform. Alexander Mazein, Marcio Luis Acencio, Irina Balaur, Adrien Rougny, Danielle Welter, Anna Niarakis, Diana Ramirez Ardila, Ugur Dogrusoz, Piotr Gawron, Venkata P. Satagopam, Wei Gu, Andreas Kremer, Reinhard Schneider, Marek Ostaszewski
2023	J	`jnl`	Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses. Frontiers Bioinform. Ahmed Abdelmonem Hemedan, Reinhard Schneider, Marek Ostaszewski
2023	J	`jnl`	Visualization of automatically combined disease maps and pathway diagrams for rare diseases. Frontiers Bioinform. Piotr Gawron, David Hoksza, Janet Piñero, María Peña-Chilet, Marina Esteban-Medina, Jose Luis Fernandez-Rueda, Vincenza Colonna, Ewa Smula, Laurent Heirendt, François Ancien, Valentin Grouès, Venkata P. Satagopam, Reinhard Schneider, Joaquín Dopazo, Laura I. Furlong, Marek Ostaszewski
2021	J	`jnl`	Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2021	J	`jnl`	Machine Learning to Support the Presentation of Complex Pathway Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. Sune S. Nielsen, Marek Ostaszewski, Fintan McGee, David Hoksza, Simone Zorzan
2021	J	`jnl`	Mechanistic modeling of the SARS-CoV-2 disease map. BioData Min. Kinza Rian, Marina Esteban-Medina, Marta R. Hidalgo, Cankut Çubuk, Matias M. Falco, Carlos Loucera, Devrim Gunyel, Marek Ostaszewski, María Peña-Chilet, Joaquín Dopazo
2021	J	`jnl`	Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Briefings Bioinform. Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez-Rodriguez, Marek Ostaszewski, Reinhard Schneider
2021	J	`jnl`	Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. Briefings Bioinform. Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
2020	J	`jnl`	Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2020	J	`jnl`	RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database J. Biol. Databases Curation Vidisha Singh, George D. Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira, Anna Niarakis
2019	J	`jnl`	Community-driven roadmap for integrated disease maps. Briefings Bioinform. Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
2019	J	`jnl`	MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider
2018	J	`jnl`	Clustering approaches for visual knowledge exploration in molecular interaction networks. BMC Bioinform. Marek Ostaszewski, Emmanuel Kieffer, Grégoire Danoy, Reinhard Schneider, Pascal Bouvry
2018	J	`jnl`	MolArt: a molecular structure annotation and visualization tool. Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Reinhard Schneider
2018	—	`conf`	Single and Multiobjective Evolutionary Algorithms for Clustering Biomedical Information with Unknown Number of Clusters. BIOMA María Eugenia Curi, Lucía Carozzi, Renzo Massobrio, Sergio Nesmachnow, Grégoire Danoy, Marek Ostaszewski, Pascal Bouvry
2016	J	`jnl`	Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. Big Data Venkata P. Satagopam, Wei Gu, Serge Eifes, Piotr Gawron, Marek Ostaszewski, Stephan Gebel, Adriano Barbosa-Silva, Rudi Balling, Reinhard Schneider
2014	—	`conf`	Visualization and classification of protein secondary structures using Self-Organizing Maps. MCDM Christian Grévisse, Ian Muller, Juan Luis Jiménez Laredo, Marek Ostaszewski, Grégoire Danoy, Pascal Bouvry
2009	A	`conf`	Multiobjective classification with moGEP: an application in the network traffic domain. GECCO Marek Ostaszewski, Pascal Bouvry, Franciszek Seredynski
2008	A	`conf`	Adaptive and dynamic intrusion detection by means of idiotypic networks paradigm. IPDPS Marek Ostaszewski, Pascal Bouvry, Franciszek Seredynski
2008	B	`conf`	An approach to intrusion detection by means of idiotypic networks paradigm. IEEE Congress on Evolutionary Computation Marek Ostaszewski, Pascal Bouvry, Franciszek Seredynski
2008	A	`conf`	Denial of service detection and analysis using idiotypic networks paradigm. GECCO Marek Ostaszewski, Pascal Bouvry, Franciszek Seredynski
2007	J	`jnl`	Coevolutionary-based Mechanisms for Network Anomaly Detection. J. Math. Model. Algorithms Marek Ostaszewski, Franciszek Seredynski, Pascal Bouvry
2006	A	`conf`	A nonself space approach to network anomaly detection. IPDPS Marek Ostaszewski, Franciszek Seredynski, Pascal Bouvry
2006	A	`conf`	Immune anomaly detection enhanced with evolutionary paradigms. GECCO Marek Ostaszewski, Franciszek Seredynski, Pascal Bouvry
2006	—	`conf`	Network Traffic Analysis Using Immunological and Evolutionary Paradigms. Intelligent Information Systems Marek Ostaszewski, Franciszek Seredynski, Pascal Bouvry